spatialLIBD
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LieberInstitute
[BUG] fetch_data(): Not all rnames found or unique
Describe the bug
Thank you for your work! I wanted to report that no data object is returned with `fetch_data(type='spe').
Provide a minimally reproducible example (reprex)
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("spatialLIBD")
library(spatialLIBD)
spe <- fetch_data(type = "spe")
results in
snapshotDate(): 2024-04-29
adding rname 'https://www.dropbox.com/s/f4wcvtdq428y73p/Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata?dl=1'
|======================================================================| 100%
|======================================================================| 100%
Error in BiocFileCache::bfcrpath(bfc, url) :
not all 'rnames' found or unique.
In addition: Warning message:
In value[[3L]](cond) :
trying to add rname 'https://www.dropbox.com/s/f4wcvtdq428y73p/Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata?dl=1' produced error:
HTTP/2 stream 1 was not closed cleanly: PROTOCOL_ERROR (err 1)
> str(spe)
Error: object 'spe' not found
Expected behavior
spe object is created.
R Session Information
options(width = 120)
> sessionInfo()
R version 4.4.0 (2024-04-24)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.5
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/New_York
tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] spatialLIBD_1.16.2 SpatialExperiment_1.14.0
[3] SingleCellExperiment_1.26.0 SummarizedExperiment_1.34.0
[5] Biobase_2.64.0 GenomicRanges_1.56.1
[7] GenomeInfoDb_1.40.1 IRanges_2.38.1
[9] S4Vectors_0.42.1 BiocGenerics_0.50.0
[11] MatrixGenerics_1.16.0 matrixStats_1.4.1
[13] BiocManager_1.30.25
loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-3 jsonlite_1.8.9
[3] magrittr_2.0.3 ggbeeswarm_0.7.2
[5] magick_2.8.5 BiocIO_1.14.0
[7] fields_16.3 zlibbioc_1.50.0
[9] vctrs_0.6.5 memoise_2.0.1
[11] config_0.3.2 Rsamtools_2.20.0
[13] DelayedMatrixStats_1.26.0 paletteer_1.6.0
[15] RCurl_1.98-1.16 benchmarkme_1.0.8
[17] htmltools_0.5.8.1 S4Arrays_1.4.1
[19] AnnotationHub_3.12.0 curl_5.2.3
[21] BiocNeighbors_1.22.0 SparseArray_1.4.8
[23] sass_0.4.9 bslib_0.8.0
[25] htmlwidgets_1.6.4 plotly_4.10.4
[27] cachem_1.1.0 GenomicAlignments_1.40.0
[29] mime_0.12 lifecycle_1.0.4
[31] iterators_1.0.14 pkgconfig_2.0.3
[33] rsvd_1.0.5 Matrix_1.7-0
[35] R6_2.5.1 fastmap_1.2.0
[37] GenomeInfoDbData_1.2.12 shiny_1.9.1
[39] digest_0.6.37 colorspace_2.1-1
[41] rematch2_2.1.2 AnnotationDbi_1.66.0
[43] scater_1.32.1 irlba_2.3.5.1
[45] ExperimentHub_2.12.0 RSQLite_2.3.7
[47] beachmat_2.20.0 filelock_1.0.3
[49] fansi_1.0.6 httr_1.4.7
[51] abind_1.4-8 compiler_4.4.0
[53] withr_3.0.1 bit64_4.5.2
[55] doParallel_1.0.17 attempt_0.3.1
[57] BiocParallel_1.38.0 viridis_0.6.5
[59] DBI_1.2.3 maps_3.4.2
[61] sessioninfo_1.2.2 rappdirs_0.3.3
[63] DelayedArray_0.30.1 rjson_0.2.23
[65] tools_4.4.0 vipor_0.4.7
[67] beeswarm_0.4.0 httpuv_1.6.15
[69] glue_1.8.0 restfulr_0.0.15
[71] promises_1.3.0 grid_4.4.0
[73] generics_0.1.3 gtable_0.3.5
[75] tidyr_1.3.1 data.table_1.16.0
[77] ScaledMatrix_1.12.0 BiocSingular_1.20.0
[79] utf8_1.2.4 XVector_0.44.0
[81] stringr_1.5.1 ggrepel_0.9.6
[83] BiocVersion_3.19.1 foreach_1.5.2
[85] pillar_1.9.0 spam_2.11-0
[87] limma_3.60.6 later_1.3.2
[89] benchmarkmeData_1.0.4 dplyr_1.1.4
[91] BiocFileCache_2.12.0 lattice_0.22-6
[93] rtracklayer_1.64.0 bit_4.5.0
[95] tidyselect_1.2.1 locfit_1.5-9.10
[97] Biostrings_2.72.1 scuttle_1.14.0
[99] gridExtra_2.3 edgeR_4.2.1
[101] statmod_1.5.0 DT_0.33
[103] stringi_1.8.4 UCSC.utils_1.0.0
[105] lazyeval_0.2.2 yaml_2.3.10
[107] shinyWidgets_0.8.7 codetools_0.2-20
[109] tibble_3.2.1 cli_3.6.3
[111] xtable_1.8-4 jquerylib_0.1.4
[113] munsell_0.5.1 golem_0.5.1
[115] Rcpp_1.0.13 dbplyr_2.5.0
[117] png_0.1-8 XML_3.99-0.17
[119] parallel_4.4.0 ggplot2_3.5.1
[121] blob_1.2.4 dotCall64_1.2
[123] sparseMatrixStats_1.16.0 bitops_1.0-9
[125] viridisLite_0.4.2 scales_1.3.0
[127] purrr_1.0.2 crayon_1.5.3
[129] rlang_1.1.4 cowplot_1.1.3
[131] KEGGREST_1.44.1
Indicate whether BiocManager::valid() returns TRUE.
- [x]
BiocManager::valid()isTRUE
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